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RiceLncPedia: a curated knowledgebase of rice Long non-coding RNAs
Summary
Sequence
Coding Potentia
Genome Browser
Expression
Variation
Sequence

>Osa04LNT0253300.1

GTCTAGTATGAATTATTACATCATAAGCCCGCAGGCACAGTCTTAAATCATCGGACCGAGCGGTCCGGAATACATTCCAAAAACAGAAGTAGGTAAGGCAGCGGAGTTAAGGCAGCGGCACGCCATTGCCACAGGCAACGACCGTACTAAGACCTACTGAGCGCCATCGTCTTCATCTCCCTCCTGGTAGTAGGCATAGGGATCCTCCGAAGCTTCATCTCCCGCTTCTTGCTCAAGGTCTTGGGGGTCTTGGCCTTCACTTGGATCCGCAACTCCCTCGGGCTTTTATAAAAGAAGCATCCACCAAGGTACAAGATCGGAGAGAGCGCCGACACTCTGGCATTCCTCTGGGACTGCCATGGAAAGAGTGCTCACAACTCCAACACTCCTCCGGAACTCCTTATAAAGAACTCCGAACTTTGGGGCACTCCTTTTGGAGCTTTCCCTCACCCTCTTCCCATATTCTAACTCTACGAGAGAGTAGCCTAGATATCAAAGTGAGTTGTACTCCAC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.327178
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0253300.1 4 9919884 T C
Osa04LNT0253300.1 4 9923874 C A
Osa04LNT0253300.1 4 9924438 T C
Osa04LNT0253300.1 4 9924491 G A
Osa04LNT0253300.1 4 9924694 A G
Osa04LNT0253300.1 4 9924713 A G
Osa04LNT0253300.1 4 9924740 A G
Osa04LNT0253300.1 4 9924857 T C
Osa04LNT0253300.1 4 9925754 T C
Osa04LNT0253300.1 4 9925852 T C
Osa04LNT0253300.1 4 9926024 G A
Osa04LNT0253300.1 4 9926140 G A
Osa04LNT0253300.1 4 9925686 A G
Osa04LNT0253300.1 4 9924721 A G
Osa04LNT0253300.1 4 9925502 A C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0253300.1 osa-miR444a-3p.1 Translation 5.0 22.961 1 21
Osa04LNT0253300.1 osa-miR395o Cleavage 4.0 21.615 1 21
Osa04LNT0253300.1 osa-miR395w Cleavage 4.5 21.615 1 22
Osa04LNT0253300.1 osa-miR444d.1 Translation 5.0 22.961 1 21
Osa04LNT0253300.1 osa-miR2105 Translation 3.0 15.505 1 20
Osa04LNT0253300.1 osa-miR5506 Translation 3.0 23.892 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0253300.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0253300.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0253300.1 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
Osa04LNT0253300.1 4 qPEN-4 Morphological trait Panicle/flower RG190 RG908
Osa04LNT0253300.1 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0253300.1 4 nan Morphological trait Root RM261 RZ69
Osa04LNT0253300.1 4 nan Morphological trait Root RM261 RZ69
Osa04LNT0253300.1 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0253300.1 4 qSNP-4a Morphological trait Panicle/flower RM401 RM335
Osa04LNT0253300.1 4 qCER4-1 Morphological trait Shoot/Seedling RG190 RZ69
pre-miRNA
Transcript ID Pre-miRNA Identity(%) Alignment Length Pre-miRNA start Pre-miRNA end E-value Bitscore
GWAS
Transcript ID Chromosome Locus Trait Value Plus Minus